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Beta-diversity analysis


Where we analyse the effect of a factor on shared diversity

Author: Adrien Taudière

Date: October 29, 2024

See the documentation of the MiscMetabar package for example of btea diversity analysis.

Code
if(base::interactive()) {
  params <- rmarkdown::yaml_front_matter(here::here("analysis/03_beta_diversity.qmd"))$params
}
factor_of_interest <- params$factor_of_interest
Code
library(knitr)
library(targets)
library(MiscMetabar)
here::i_am("analysis/03_beta_diversity.qmd")
source(here::here("R/styles.R"))
Code
d_pq <- clean_pq(tar_read("d_vs", store=here::here("_targets/")))
Cleaning suppress 2 taxa and 1 samples.
Code
formattable_pq(
    subset_samples(d_pq, Type %in% c("Mix", "Mono")),
    factor_of_interest,
    min_nb_seq_taxa = 1000, 
    lev_col_taxa = "Family",
    taxonomic_levels=c("Order", "Family", "Genus"),
    log10trans = TRUE,

  )
Cleaning suppress 0 taxa (  ) and 0 sample(s) (  ).
Number of non-matching ASV 0
Number of matching ASV 1145
Number of filtered-out ASV 803
Number of kept ASV 342
Number of kept samples 437
Cleaning suppress 0 taxa and 0 samples.
Joining with `by = join_by(OTU)`
OTU Order Family Genus Mix Mono proportion_samp nb_seq
Taxa_2 Glomerales Claroideoglomeraceae Claroideoglomus 5.71 5.89 0.84 6.11
Taxa_1 NA NA NA 5.72 5.87 0.71 6.10
Taxa_21 NA NA NA 5.62 5.71 0.89 5.97
Taxa_3 Glomerales Glomeraceae Glomus 5.49 5.65 0.85 5.88
Taxa_13 Glomerales Claroideoglomeraceae Claroideoglomus 5.45 5.55 0.79 5.81
Taxa_11 Glomerales Glomeraceae Glomus 5.28 5.62 0.67 5.78
Taxa_5 Glomerales Glomeraceae Glomus 5.42 5.48 0.81 5.75
Taxa_18 NA NA NA 5.36 5.48 0.90 5.73
Taxa_20 Glomerales NA NA 5.34 5.47 0.51 5.71
Taxa_12 Glomerales Glomeraceae Glomus 5.41 5.39 0.69 5.70
Taxa_6 Glomerales Glomeraceae Glomus 5.23 5.53 0.80 5.70
Taxa_17 Glomerales Glomeraceae Glomus 5.17 5.50 0.83 5.67
Taxa_7 Glomerales Glomeraceae Glomus 5.28 5.42 0.74 5.66
Taxa_9 Glomerales Glomeraceae Glomus 5.26 5.42 0.65 5.65
Taxa_8 Glomerales Glomeraceae Glomus 5.17 5.47 0.66 5.64
Taxa_10 Glomerales Glomeraceae Glomus 5.29 5.36 0.86 5.63
Taxa_15 NA NA NA 5.19 5.30 0.59 5.55
Taxa_14 Glomerales Glomeraceae Glomus 5.21 5.26 0.51 5.53
Taxa_16 Glomerales Glomeraceae Glomus 5.14 5.27 0.66 5.51
Taxa_23 Glomerales Claroideoglomeraceae Claroideoglomus 5.13 5.25 0.69 5.50
Taxa_19 NA NA NA 5.07 5.16 0.54 5.42
Taxa_36 Glomerales Glomeraceae Glomus 5.04 5.16 0.39 5.40
Taxa_22 NA NA NA 4.73 5.29 0.58 5.39
Taxa_27 NA NA NA 4.97 5.15 0.95 5.37
Taxa_28 Glomerales Glomeraceae Glomus 4.97 5.10 0.69 5.34
Taxa_24 Glomerales Glomeraceae Glomus 4.90 5.10 0.36 5.32
Taxa_34 Glomerales NA NA 4.91 5.10 0.54 5.32
Taxa_41 Glomerales Glomeraceae Glomus 4.91 5.05 0.78 5.29
Taxa_29 NA NA NA 4.90 5.05 0.89 5.28
Taxa_30 NA NA NA 4.88 5.07 0.75 5.28
Taxa_31 Glomerales Glomeraceae Glomus 4.88 5.05 0.85 5.28
Taxa_32 Glomerales NA NA 4.87 5.04 0.92 5.26
Taxa_49 NA NA NA 4.76 5.03 0.56 5.22
Taxa_35 NA NA NA 4.79 5.01 0.79 5.21
Taxa_48 Glomerales NA NA 4.76 5.00 0.48 5.20
Taxa_37 Glomerales Glomeraceae Glomus 4.76 4.99 0.54 5.19
Taxa_38 NA NA NA 4.82 4.91 0.75 5.17
Taxa_42 Glomerales NA NA 4.75 4.90 0.53 5.13
Taxa_53 Glomerales Glomeraceae Glomus 4.82 4.74 0.55 5.08
Taxa_59 Glomerales NA NA 4.65 4.83 0.71 5.05
Taxa_72 NA NA NA 4.69 4.80 0.41 5.05
Taxa_45 Glomerales Glomeraceae Glomus 3.68 5.01 0.28 5.03
Taxa_52 NA NA NA 4.64 4.77 0.54 5.01
Taxa_97 Glomerales Glomeraceae Glomus 4.68 4.73 0.54 5.01
Taxa_47 Glomerales Glomeraceae Glomus 4.53 4.80 0.71 4.99
Taxa_61 Glomerales Glomeraceae NA 4.60 4.75 0.49 4.98
Taxa_55 NA NA NA 4.70 4.63 0.59 4.97
Taxa_63 NA NA NA 4.55 4.76 0.46 4.97
Taxa_51 Glomerales Glomeraceae Glomus 4.60 4.69 0.53 4.95
Taxa_54 Glomerales Glomeraceae Glomus 4.56 4.66 0.43 4.91
Taxa_58 NA NA NA 4.55 4.65 0.70 4.90
Taxa_57 Glomerales Glomeraceae Glomus 4.54 4.62 0.24 4.89
Taxa_60 NA NA NA 4.47 4.62 0.73 4.85
Taxa_65 NA NA NA 4.41 4.59 0.58 4.81
Taxa_113 NA NA NA 4.37 4.59 0.42 4.80
Taxa_67 NA NA NA 4.13 4.69 0.32 4.80
Taxa_68 Glomerales Glomeraceae Glomus 4.56 4.43 0.24 4.80
Taxa_87 NA NA NA 4.50 4.50 0.22 4.80
Taxa_70 NA NA NA 4.37 4.55 0.73 4.77
Taxa_66 NA NA NA 4.43 4.49 0.41 4.76
Taxa_69 NA NA NA 4.37 4.54 0.52 4.76
Taxa_79 NA NA NA 4.38 4.46 0.71 4.72
Taxa_73 NA NA NA 4.31 4.46 0.57 4.69
Taxa_74 NA NA NA 4.22 4.50 0.34 4.68
Taxa_75 Glomerales Claroideoglomeraceae Claroideoglomus 4.31 4.43 0.46 4.67
Taxa_81 Glomerales NA NA 4.31 4.41 0.41 4.66
Taxa_151 NA NA NA 3.93 4.55 0.22 4.65
Taxa_77 NA NA NA 4.22 4.44 0.52 4.65
Taxa_99 Glomerales NA NA 4.30 4.38 0.77 4.64
Taxa_80 NA NA NA 4.24 4.39 0.65 4.62
Taxa_106 Glomerales Glomeraceae Glomus 4.24 4.37 0.35 4.61
Taxa_129 NA NA NA 4.27 4.35 0.62 4.61
Taxa_82 Glomerales Glomeraceae Glomus 4.16 4.39 0.33 4.60
Taxa_138 NA NA NA 4.31 4.27 0.32 4.59
Taxa_133 Glomerales Glomeraceae Glomus 4.22 4.33 0.29 4.58
Taxa_86 NA NA NA 4.14 4.37 0.30 4.57
Taxa_94 NA NA NA 4.11 4.38 0.46 4.57
Taxa_110 NA NA NA 4.17 4.33 0.43 4.56
Taxa_90 NA NA NA 4.26 4.23 0.03 4.55
Taxa_91 NA NA NA 4.18 4.30 0.80 4.55
Taxa_128 NA NA NA 4.22 4.25 0.45 4.54
Taxa_139 NA NA NA 4.21 4.26 0.44 4.54
Taxa_98 Glomerales Claroideoglomeraceae Claroideoglomus 4.15 4.31 0.37 4.54
Taxa_92 Glomerales Glomeraceae Glomus 4.27 4.17 0.38 4.53
Taxa_95 NA NA NA 4.16 4.29 0.54 4.53
Taxa_102 NA NA NA 1.63 4.51 0.01 4.51
Taxa_123 NA NA NA 3.94 4.37 0.45 4.51
Taxa_101 Glomerales Glomeraceae Glomus 4.10 4.28 0.35 4.50
Taxa_126 Glomerales Glomeraceae Glomus 4.08 4.28 0.45 4.49
Taxa_239 Glomerales Glomeraceae Glomus 4.10 4.26 0.49 4.49
Taxa_108 NA NA NA 4.06 4.27 0.56 4.48
Taxa_145 NA NA NA 4.11 4.24 0.41 4.48
Taxa_191 Glomerales Glomeraceae Glomus 4.11 4.23 0.47 4.48
Taxa_109 NA NA NA 4.08 4.22 0.35 4.46
Taxa_111 NA NA NA 4.10 4.21 0.46 4.46
Taxa_112 Glomerales Glomeraceae Glomus 4.03 4.25 0.30 4.45
Taxa_156 NA NA NA 4.11 4.17 0.42 4.44
Taxa_163 Glomerales Glomeraceae Glomus 4.09 4.15 0.52 4.43
Taxa_188 Glomerales NA NA 4.09 4.16 0.51 4.43
Taxa_115 NA NA NA 4.07 4.16 0.85 4.42
Taxa_120 Glomerales Glomeraceae Glomus 3.91 4.23 0.31 4.40
Taxa_195 NA NA NA 4.04 4.14 0.40 4.39
Taxa_233 Glomerales Glomeraceae Glomus 4.06 4.12 0.34 4.39
Taxa_166 NA NA NA 3.97 4.15 0.58 4.37
Taxa_137 Glomerales Glomeraceae Glomus 4.16 3.88 0.26 4.34
Taxa_130 Glomerales Glomeraceae Glomus 2.37 4.32 0.08 4.32
Taxa_147 NA NA NA 3.99 4.04 0.32 4.32
Taxa_164 NA NA NA 3.97 4.04 0.42 4.31
Taxa_132 Glomerales Glomeraceae Glomus 3.98 4.01 0.18 4.30
Taxa_140 Glomerales Glomeraceae Glomus 3.94 4.02 0.46 4.28
Taxa_165 Glomerales Glomeraceae Glomus 3.83 4.09 0.26 4.28
Taxa_184 NA NA NA 3.85 4.09 0.37 4.28
Taxa_136 NA NA NA 3.82 4.07 0.44 4.26
Taxa_143 NA NA NA 3.92 3.97 0.37 4.24
Taxa_148 NA NA NA 3.81 4.04 0.35 4.24
Taxa_150 Glomerales Glomeraceae Glomus 3.84 3.98 0.25 4.22
Taxa_153 NA NA NA 3.70 4.02 0.28 4.19
Taxa_187 NA NA NA 3.73 4.00 0.33 4.19
Taxa_235 NA NA NA 3.76 3.99 0.26 4.19
Taxa_157 NA NA NA 3.62 4.04 0.25 4.18
Taxa_312 NA NA NA 3.79 3.93 0.37 4.17
Taxa_175 NA NA NA 3.73 3.94 0.34 4.15
Taxa_204 Glomerales Glomeraceae Glomus 3.83 3.87 0.32 4.15
Taxa_181 NA NA NA 3.80 3.83 0.26 4.12
Taxa_176 Glomerales Glomeraceae Glomus 3.69 3.86 0.30 4.08
Taxa_179 Glomerales Glomeraceae Glomus 3.87 3.67 0.12 4.08
Taxa_199 Glomerales NA NA 3.73 3.83 0.41 4.08
Taxa_206 NA NA NA 3.73 3.81 0.19 4.08
Taxa_264 NA NA NA 3.59 3.91 0.22 4.08
Taxa_190 NA NA NA 3.47 3.94 0.21 4.07
Taxa_220 Glomerales Glomeraceae Glomus 3.63 3.87 0.14 4.07
Taxa_183 Glomerales Glomeraceae Glomus 3.69 3.82 0.29 4.06
Taxa_185 NA NA NA 3.72 3.80 0.37 4.06
Taxa_217 Glomerales NA NA 3.56 3.89 0.13 4.06
Taxa_236 NA NA NA 3.55 3.90 0.07 4.06
Taxa_259 NA NA NA 3.66 3.84 0.33 4.06
Taxa_271 NA NA NA 3.75 3.77 0.25 4.06
Taxa_294 NA NA NA 3.74 3.79 0.13 4.06
Taxa_192 Glomerales NA NA 3.69 3.80 0.27 4.05
Taxa_194 Glomerales NA NA 3.50 3.89 0.11 4.04
Taxa_213 Glomerales Glomeraceae Glomus 3.56 3.86 0.15 4.04
Taxa_310 NA NA NA 3.46 3.90 0.17 4.04
Taxa_200 Glomerales Glomeraceae Glomus 3.63 3.79 0.28 4.02
Taxa_214 NA NA NA 3.83 3.58 0.03 4.02
Taxa_202 Glomerales NA NA 3.62 3.79 0.24 4.01
Taxa_205 Glomerales Glomeraceae Glomus 3.67 3.75 0.14 4.01
Taxa_207 Glomerales NA NA 3.65 3.74 0.16 4.00
Taxa_234 NA NA NA 3.36 3.88 0.19 4.00
Taxa_248 NA NA NA 3.64 3.76 0.26 4.00
Taxa_209 Glomerales Glomeraceae Glomus 3.23 3.91 0.20 3.99
Taxa_211 Glomerales Glomeraceae Glomus 3.69 3.70 0.21 3.99
Taxa_212 Glomerales Glomeraceae Glomus 3.68 3.71 0.25 3.99
Taxa_288 NA NA NA 3.59 3.77 0.33 3.99
Taxa_229 NA NA NA 3.64 3.70 0.29 3.97
Taxa_258 Glomerales Glomeraceae Glomus 3.58 3.75 0.17 3.97
Taxa_222 Glomerales NA NA 3.56 3.73 0.28 3.96
Taxa_215 Glomerales Glomeraceae Glomus 3.65 3.65 0.19 3.95
Taxa_223 Glomerales Glomeraceae Glomus 3.56 3.73 0.25 3.95
Taxa_245 Glomerales Glomeraceae Glomus 3.56 3.71 0.42 3.94
Taxa_269 NA NA NA 3.69 3.59 0.25 3.94
Taxa_261 Glomerales Glomeraceae Glomus 3.55 3.67 0.18 3.92
Taxa_366 Glomerales Glomeraceae Glomus 3.47 3.73 0.14 3.92
Taxa_257 NA NA NA 3.58 3.60 0.15 3.89
Taxa_339 NA NA NA 3.59 3.59 0.21 3.89
Taxa_328 NA NA NA 2.91 3.82 0.03 3.87
Taxa_228 NA NA NA 3.48 3.60 0.29 3.85
Taxa_246 NA NA NA 3.57 3.53 0.15 3.85
Taxa_251 NA NA NA 3.59 3.52 0.18 3.85
Taxa_252 Glomerales NA NA 3.52 3.57 0.35 3.85
Taxa_263 NA NA NA 3.47 3.60 0.09 3.84
Taxa_341 NA NA NA 3.28 3.70 0.06 3.84
Taxa_253 Glomerales Glomeraceae Glomus 3.59 3.46 0.01 3.83
Taxa_292 NA NA NA 3.53 3.50 0.38 3.82
Taxa_322 Glomerales Glomeraceae Glomus 3.34 3.65 0.18 3.82
Taxa_249 Glomerales Glomeraceae Glomus 3.10 3.72 0.04 3.81
Taxa_365 Glomerales Glomeraceae Glomus 3.39 3.60 0.19 3.81
Taxa_293 NA NA NA 3.48 3.51 0.19 3.80
Taxa_332 Glomerales Claroideoglomeraceae Claroideoglomus 3.43 3.52 0.18 3.78
Taxa_266 NA NA NA 3.42 3.51 0.30 3.77
Taxa_276 NA NA NA 3.26 3.60 0.22 3.77
Taxa_274 NA NA NA 3.38 3.52 0.19 3.76
Taxa_289 NA NA NA 3.70 2.85 0.01 3.76
Taxa_278 Glomerales NA NA 3.28 3.57 0.04 3.75
Taxa_279 Glomerales Glomeraceae Glomus 3.56 3.30 0.12 3.75
Taxa_349 NA NA NA 3.15 3.63 0.06 3.75
Taxa_361 Glomerales Glomeraceae Glomus 3.44 3.46 0.10 3.75
Taxa_323 NA NA NA 3.25 3.58 0.11 3.74
Taxa_363 Glomerales Glomeraceae Glomus 3.47 3.40 0.14 3.74
Taxa_285 NA NA NA 3.37 3.48 0.18 3.73
Taxa_500 Glomerales Glomeraceae Glomus 3.24 3.56 0.11 3.73
Taxa_354 NA NA NA 3.43 3.40 0.05 3.72
Taxa_296 Glomerales Glomeraceae Glomus 3.24 3.50 0.13 3.69
Taxa_301 NA NA NA 3.40 3.35 0.17 3.68
Taxa_302 Glomerales Glomeraceae Glomus 3.36 3.39 0.08 3.68
Taxa_313 NA NA NA 3.16 3.52 0.17 3.68
Taxa_319 Glomerales Glomeraceae Glomus 3.24 3.48 0.12 3.68
Taxa_304 NA NA NA 3.54 3.11 0.08 3.67
Taxa_305 NA NA NA 3.36 3.39 0.15 3.67
Taxa_318 NA NA NA 3.23 3.48 0.14 3.67
Taxa_309 NA NA NA 3.30 3.42 0.10 3.66
Taxa_368 Glomerales Glomeraceae Glomus 3.20 3.48 0.10 3.66
Taxa_389 Glomerales Glomeraceae Glomus 3.11 3.52 0.05 3.66
Taxa_317 NA NA NA 2.14 3.64 0.02 3.65
Taxa_345 NA NA NA 3.27 3.41 0.16 3.65
Taxa_316 Glomerales Glomeraceae Glomus 3.23 3.43 0.11 3.64
Taxa_396 Glomerales NA NA 3.20 3.43 0.29 3.63
Taxa_558 Glomerales Glomeraceae Glomus 3.27 3.37 0.13 3.63
Taxa_329 NA NA NA 3.28 3.34 0.08 3.61
Taxa_362 Glomerales Glomeraceae Glomus 3.15 3.40 0.22 3.60
Taxa_370 NA NA NA 3.26 3.35 0.16 3.60
Taxa_342 Glomerales Glomeraceae Glomus 3.20 3.36 0.16 3.59
Taxa_337 Paraglomerales Paraglomeraceae Paraglomus 3.19 3.36 0.20 3.58
Taxa_344 Glomerales Glomeraceae Glomus 3.21 3.31 0.14 3.57
Taxa_346 NA NA NA 3.09 3.40 0.30 3.57
Taxa_348 NA NA NA 3.22 3.29 0.12 3.56
Taxa_357 NA NA NA 3.49 2.67 0.05 3.55
Taxa_588 Diversisporales NA NA 3.24 3.27 0.13 3.55
Taxa_352 NA NA NA 2.03 3.53 0.04 3.54
Taxa_358 Glomerales NA NA 3.08 3.36 0.03 3.54
Taxa_378 Glomerales Glomeraceae Glomus 3.20 3.25 0.30 3.53
Taxa_427 NA NA NA 2.44 3.49 0.09 3.53
Taxa_430 Glomerales Glomeraceae Glomus 2.71 3.45 0.05 3.52
Taxa_433 NA NA NA 3.24 3.19 0.18 3.52
Taxa_364 NA NA NA 3.45 2.65 0.02 3.51
Taxa_376 NA NA NA 3.21 3.20 0.15 3.51
Taxa_520 NA NA NA 3.19 3.23 0.14 3.51
Taxa_553 Glomerales NA NA 1.89 3.50 0.03 3.51
Taxa_367 NA NA NA 3.09 3.29 0.28 3.50
Taxa_373 Glomerales Glomeraceae Glomus 3.12 3.24 0.13 3.49
Taxa_404 Glomerales Glomeraceae Glomus 2.92 3.35 0.04 3.49
Taxa_496 Glomerales NA NA 3.09 3.27 0.10 3.49
Taxa_559 Glomerales Glomeraceae Glomus 0.00 3.49 0.01 3.49
Taxa_403 NA NA NA 3.23 3.12 0.13 3.48
Taxa_420 NA NA NA 3.20 3.15 0.15 3.48
Taxa_394 Glomerales Glomeraceae Glomus 3.23 3.11 0.09 3.47
Taxa_424 NA NA NA 3.04 3.26 0.07 3.47
Taxa_482 Glomerales NA NA 3.10 3.24 0.09 3.47
Taxa_379 Glomerales Glomeraceae Glomus 3.15 3.16 0.30 3.46
Taxa_393 Glomerales Glomeraceae Glomus 3.20 3.09 0.08 3.45
Taxa_390 NA NA NA 2.75 3.34 0.07 3.44
Taxa_407 NA NA NA 3.11 3.15 0.14 3.43
Taxa_412 NA NA NA 3.14 3.12 0.16 3.43
Taxa_402 NA NA NA 3.12 3.11 0.19 3.42
Taxa_406 Glomerales Glomeraceae Glomus 3.42 0.00 0.00 3.42
Taxa_527 NA NA NA 3.02 3.20 0.07 3.42
Taxa_545 NA NA NA 3.10 3.11 0.06 3.41
Taxa_408 Glomerales Glomeraceae Glomus 2.52 3.34 0.06 3.40
Taxa_409 Glomerales Glomeraceae Glomus 2.93 3.22 0.04 3.40
Taxa_418 NA NA NA 3.32 2.62 0.01 3.40
Taxa_419 NA NA NA 3.05 3.15 0.06 3.40
Taxa_463 Glomerales Glomeraceae Glomus 3.12 3.07 0.06 3.40
Taxa_561 NA NA NA 3.18 2.99 0.06 3.40
Taxa_422 NA NA NA 2.82 3.25 0.09 3.39
Taxa_648 NA NA NA 2.83 3.19 0.07 3.35
Taxa_460 NA NA NA 2.95 3.11 0.11 3.34
Taxa_533 Glomerales Glomeraceae Glomus 3.01 3.07 0.08 3.34
Taxa_440 NA NA NA 2.88 3.14 0.03 3.33
Taxa_441 Glomerales Glomeraceae Glomus 2.78 3.18 0.08 3.33
Taxa_443 NA NA NA 2.41 3.27 0.01 3.33
Taxa_591 Glomerales Glomeraceae Glomus 2.95 3.10 0.08 3.33
Taxa_442 Glomerales Glomeraceae Glomus 3.08 2.95 0.05 3.32
Taxa_715 NA NA NA 3.09 2.93 0.06 3.32
Taxa_484 NA NA NA 2.90 3.11 0.11 3.31
Taxa_480 NA NA NA 2.89 3.08 0.14 3.30
Taxa_556 Glomerales Glomeraceae Glomus 2.84 3.12 0.08 3.30
Taxa_450 NA NA NA 3.13 2.78 0.03 3.29
Taxa_453 NA NA NA 2.78 3.13 0.05 3.29
Taxa_454 Glomerales Glomeraceae Glomus 3.01 2.97 0.07 3.29
Taxa_459 Diversisporales NA NA 2.83 3.11 0.07 3.29
Taxa_612 NA NA NA 2.77 3.13 0.07 3.29
Taxa_462 Glomerales Glomeraceae Glomus 3.05 2.88 0.08 3.28
Taxa_465 Glomerales NA NA 2.88 3.06 0.07 3.28
Taxa_532 NA NA NA 2.78 3.10 0.25 3.27
Taxa_535 NA NA NA 3.08 2.80 0.05 3.26
Taxa_572 NA NA NA 2.80 3.07 0.04 3.26
Taxa_759 NA NA NA 2.85 3.05 0.13 3.26
Taxa_474 NA NA NA 2.58 3.15 0.05 3.25
Taxa_475 Glomerales Glomeraceae Glomus 0.00 3.25 0.00 3.25
Taxa_593 Glomerales Glomeraceae Glomus 2.85 3.03 0.10 3.25
Taxa_510 NA NA NA 2.82 3.03 0.06 3.24
Taxa_549 Glomerales Glomeraceae Glomus 2.79 3.04 0.19 3.23
Taxa_554 Glomerales NA NA 2.93 2.93 0.05 3.23
Taxa_585 NA NA NA 2.90 2.96 0.07 3.23
Taxa_483 NA NA NA 2.49 3.13 0.04 3.22
Taxa_485 NA NA NA 3.11 2.54 0.03 3.21
Taxa_696 Glomerales Glomeraceae Glomus 2.96 2.85 0.03 3.21
Taxa_489 NA NA NA 2.97 2.82 0.07 3.20
Taxa_498 NA NA NA 2.80 2.97 0.17 3.20
Taxa_509 Glomerales Glomeraceae Glomus 2.97 2.82 0.07 3.20
Taxa_604 NA NA NA 2.97 2.82 0.07 3.20
Taxa_495 NA NA NA 2.83 2.95 0.16 3.19
Taxa_632 NA NA NA 2.90 2.87 0.11 3.19
Taxa_640 NA NA NA 2.84 2.93 0.08 3.19
Taxa_503 NA NA NA 2.74 2.99 0.06 3.18
Taxa_512 Glomerales Glomeraceae Glomus 2.51 3.07 0.16 3.18
Taxa_570 Glomerales Glomeraceae Glomus 2.68 3.02 0.08 3.18
Taxa_608 Glomerales Glomeraceae Glomus 2.80 2.96 0.07 3.18
Taxa_1093 NA NA NA 2.85 2.90 0.13 3.17
Taxa_507 NA NA NA 2.92 2.81 0.02 3.17
Taxa_511 NA NA NA 2.93 2.80 0.07 3.17
Taxa_521 NA NA NA 2.80 2.93 0.04 3.17
Taxa_526 NA NA NA 0.00 3.17 0.01 3.17
Taxa_551 Glomerales Glomeraceae Glomus 2.82 2.91 0.14 3.17
Taxa_673 Glomerales Glomeraceae Glomus 2.57 3.04 0.09 3.17
Taxa_514 Glomerales Glomeraceae Glomus 2.81 2.92 0.03 3.16
Taxa_626 Glomerales NA NA 2.82 2.91 0.09 3.16
Taxa_586 NA NA NA 2.80 2.89 0.08 3.15
Taxa_672 Glomerales Glomeraceae Glomus 2.59 3.02 0.05 3.15
Taxa_625 Glomerales Glomeraceae Glomus 2.82 2.85 0.09 3.14
Taxa_659 NA NA NA 2.70 2.94 0.08 3.14
Taxa_660 NA NA NA 2.74 2.93 0.05 3.14
Taxa_541 Glomerales NA NA 2.98 2.60 0.07 3.13
Taxa_557 NA NA NA 2.26 3.05 0.05 3.12
Taxa_569 Glomerales Glomeraceae Glomus 0.00 3.12 0.01 3.12
Taxa_631 Glomerales Glomeraceae Glomus 2.62 2.96 0.05 3.12
Taxa_1041 NA NA NA 2.77 2.85 0.05 3.11
Taxa_540 Glomerales Glomeraceae Glomus 3.01 2.40 0.01 3.11
Taxa_547 NA NA NA 2.67 2.91 0.10 3.11
Taxa_564 Glomerales NA NA 3.09 1.71 0.01 3.10
Taxa_597 NA NA NA 2.89 2.67 0.08 3.10
Taxa_600 NA NA NA 2.57 2.96 0.09 3.10
Taxa_571 Glomerales Glomeraceae Glomus 3.09 0.00 0.00 3.09
Taxa_574 NA NA NA 2.77 2.81 0.07 3.09
Taxa_596 NA NA NA 2.82 2.76 0.02 3.09
Taxa_598 Glomerales NA NA 2.20 3.02 0.04 3.08
Taxa_583 Glomerales Glomeraceae Glomus 2.82 2.71 0.07 3.07
Taxa_850 NA NA NA 2.57 2.91 0.25 3.07
Taxa_594 Glomerales Glomeraceae Glomus 2.66 2.84 0.07 3.06
Taxa_603 NA NA NA 2.81 2.71 0.03 3.06
Taxa_599 NA NA NA 2.62 2.85 0.07 3.05
Taxa_729 NA NA NA 2.59 2.86 0.10 3.05
Taxa_605 NA NA NA 2.71 2.77 0.04 3.04
Taxa_610 NA NA NA 0.00 3.03 0.00 3.03
Taxa_611 Glomerales Glomeraceae Glomus 2.68 2.78 0.07 3.03
Taxa_613 Glomerales Glomeraceae Glomus 0.00 3.03 0.00 3.03
Taxa_615 NA NA NA 2.73 2.73 0.06 3.03
Taxa_733 NA NA NA 2.60 2.83 0.18 3.03
Taxa_619 Glomerales Glomeraceae Glomus 2.72 2.72 0.03 3.02
Taxa_624 Glomerales Claroideoglomeraceae Claroideoglomus 2.43 2.88 0.04 3.01
Taxa_687 Glomerales Glomeraceae Glomus 3.01 0.00 0.00 3.01
Taxa_679 NA NA NA 2.64 2.76 0.12 3.00
Taxa_867 NA NA NA 2.31 2.91 0.04 3.00
Code
library("vegan")
Le chargement a nécessité le package : permute
Le chargement a nécessité le package : lattice
This is vegan 2.6-8
Code
plot_ordination(d_pq, vegan::decorana(vegdist(as(otu_table(d_pq), "matrix"),
    method = "robust.aitchison"
  )), color = factor_of_interest) +
  geom_point(size = 3) +
  stat_ellipse(inherit.aes = F, aes(x = DCA1, y = DCA2, linetype = .data[[factor_of_interest]], col = .data[[factor_of_interest]])) + theme_idest() + scale_color_manual(values=idest_pal$dark_color_idest[[1]][c(5,4,2)])
Warning in plot_ordination(d_pq, vegan::decorana(vegdist(as(otu_table(d_pq), :
`Ordination species/OTU/taxa coordinate indices did not match `physeq` index
names. Setting corresponding coordinates to NULL.
Too few points to calculate an ellipse
Too few points to calculate an ellipse
Warning: Removed 2 rows containing missing values or values outside the scale range
(`geom_path()`).

Code
adonis_pq(subset_samples(d_pq, Type %in% c("Mix", "Mono")), factor_of_interest, na_remove = TRUE, correction_for_sample_size = TRUE, by = "terms")
Type
Permutation test for adonis under reduced model
Terms added sequentially (first to last)
Permutation: free
Number of permutations: 999

vegan::adonis2(formula = .formula, data = metadata, by = "terms")
             Df SumOfSqs      R2       F Pr(>F)    
sample_size   1    8.279 0.06740 31.4270  0.001 ***
Type          1    0.225 0.00183  0.8532  0.573    
Residual    434  114.326 0.93077                   
Total       436  122.829 1.00000                   
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
Code
d_pq |>
  subset_samples(Type %in% c("Mix", "Mono")) |>
biplot_pq(merge_sample_by = factor_of_interest, rarefy_after_merging = T)
Cleaning suppress 2 taxa and 0 samples.
You set `rngseed` to FALSE. Make sure you've set & recorded
 the random seed of your session for reproducibility.
See `?set.seed`
...
9OTUs were removed because they are no longer 
present in any sample after random subsampling
...
Cleaning suppress 0 taxa and 0 samples.
Scale for y is already present.
Adding another scale for y, which will replace the existing scale.

res_var <- var_par_rarperm_pq( subset_samples(d_pq, Type %in% c(“Mix”, “Mono”)), list_component = list( “Tmt” = c(“Tmt”), “Bloc” = c(“Bloc”), “Type” = c(“Type”) ), nperm = 9, dbrda_computation = TRUE )

plot_var_part_pq(res_var)




## Session Information

Session information are detailed below. More information about the machine, the system, as well as python and R packages, are available in the file <a href="data_final/information_run.txt" title="Download the informations about the hardwares and softwfares used to run these analysis" class="inline-btn"> data_final/information_run.txt </a>.

<button style="width:100%" type="button" data-bs-toggle="collapse" data-bs-target="#collapseOne" class="button-collapse">

Session Information

</button>

:::: {#collapseOne .accordion-collapse .collapse}
<div>

::: {.cell}

```{.r .cell-code}
sessionInfo()
```

::: {.cell-output .cell-output-stdout}

```
R version 4.4.1 (2024-06-14)
Platform: x86_64-pc-linux-gnu
Running under: Debian GNU/Linux 12 (bookworm)

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.11.0 
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.11.0

locale:
 [1] LC_CTYPE=fr_FR.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=fr_FR.UTF-8        LC_COLLATE=fr_FR.UTF-8    
 [5] LC_MONETARY=fr_FR.UTF-8    LC_MESSAGES=fr_FR.UTF-8   
 [7] LC_PAPER=fr_FR.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=fr_FR.UTF-8 LC_IDENTIFICATION=C       

time zone: Europe/Paris
tzcode source: system (glibc)

attached base packages:
[1] stats     graphics  grDevices datasets  utils     methods   base     

other attached packages:
 [1] vegan_2.6-8        lattice_0.22-6     permute_0.9-7      MiscMetabar_0.10.1
 [5] purrr_1.0.2        dplyr_1.1.4        dada2_1.32.0       Rcpp_1.0.13       
 [9] ggplot2_3.5.1      phyloseq_1.48.0    targets_1.8.0      knitr_1.48        

loaded via a namespace (and not attached):
  [1] bitops_1.0-9                deldir_2.0-4               
  [3] gridExtra_2.3               rlang_1.1.4                
  [5] magrittr_2.0.3              ade4_1.7-22                
  [7] matrixStats_1.4.1           compiler_4.4.1             
  [9] mgcv_1.9-1                  png_0.1-8                  
 [11] callr_3.7.6                 vctrs_0.6.5                
 [13] reshape2_1.4.4              stringr_1.5.1              
 [15] pwalign_1.0.0               pkgconfig_2.0.3            
 [17] crayon_1.5.3                fastmap_1.2.0              
 [19] backports_1.5.0             XVector_0.44.0             
 [21] labeling_0.4.3              utf8_1.2.4                 
 [23] Rsamtools_2.20.0            rmarkdown_2.28             
 [25] UCSC.utils_1.0.0            ps_1.8.0                   
 [27] xfun_0.48                   zlibbioc_1.50.0            
 [29] GenomeInfoDb_1.40.1         jsonlite_1.8.9             
 [31] biomformat_1.32.0           rhdf5filters_1.16.0        
 [33] DelayedArray_0.30.1         Rhdf5lib_1.26.0            
 [35] BiocParallel_1.38.0         jpeg_0.1-10                
 [37] parallel_4.4.1              cluster_2.1.6              
 [39] R6_2.5.1                    RColorBrewer_1.1-3         
 [41] stringi_1.8.4               GenomicRanges_1.56.2       
 [43] SummarizedExperiment_1.34.0 iterators_1.0.14           
 [45] IRanges_2.38.1              Matrix_1.7-0               
 [47] splines_4.4.1               igraph_2.1.1               
 [49] tidyselect_1.2.1            viridis_0.6.5              
 [51] abind_1.4-8                 yaml_2.3.10                
 [53] codetools_0.2-20            hwriter_1.3.2.1            
 [55] processx_3.8.4              tibble_3.2.1               
 [57] plyr_1.8.9                  Biobase_2.64.0             
 [59] withr_3.0.1                 ShortRead_1.62.0           
 [61] evaluate_1.0.1              survival_3.7-0             
 [63] RcppParallel_5.1.9          formattable_0.2.1          
 [65] Biostrings_2.72.1           pillar_1.9.0               
 [67] BiocManager_1.30.25         MatrixGenerics_1.16.0      
 [69] renv_1.0.11                 foreach_1.5.2              
 [71] stats4_4.4.1                generics_0.1.3             
 [73] rprojroot_2.0.4             S4Vectors_0.42.1           
 [75] munsell_0.5.1               scales_1.3.0               
 [77] base64url_1.4               glue_1.8.0                 
 [79] tools_4.4.1                 interp_1.1-6               
 [81] data.table_1.16.2           GenomicAlignments_1.40.0   
 [83] rhdf5_2.48.0                grid_4.4.1                 
 [85] tidyr_1.3.1                 ape_5.8                    
 [87] latticeExtra_0.6-30         colorspace_2.1-1           
 [89] nlme_3.1-165                GenomeInfoDbData_1.2.12    
 [91] cli_3.6.3                   fansi_1.0.6                
 [93] viridisLite_0.4.2           S4Arrays_1.4.1             
 [95] gtable_0.3.5                digest_0.6.37              
 [97] BiocGenerics_0.50.0         SparseArray_1.4.8          
 [99] farver_2.1.2                htmlwidgets_1.6.4          
[101] htmltools_0.5.8.1           multtest_2.60.0            
[103] lifecycle_1.0.4             here_1.0.1                 
[105] httr_1.4.7                  secretbase_1.0.3           
[107] MASS_7.3-61                
```


:::
:::



</div>
::::





:::{#quarto-navigation-envelope .hidden}
[Beta-diversity analysis]{.hidden .quarto-markdown-envelope-contents render-id="quarto-int-sidebar-title"}
[Beta-diversity analysis]{.hidden .quarto-markdown-envelope-contents render-id="quarto-int-navbar-title"}
:::



:::{#quarto-meta-markdown .hidden}
[Beta-diversity analysis]{.hidden .quarto-markdown-envelope-contents render-id="quarto-metatitle"}
[Beta-diversity analysis]{.hidden .quarto-markdown-envelope-contents render-id="quarto-twittercardtitle"}
[Beta-diversity analysis]{.hidden .quarto-markdown-envelope-contents render-id="quarto-ogcardtitle"}
[Where we analyse the effect of a factor on shared diversity]{.hidden .quarto-markdown-envelope-contents render-id="quarto-twittercarddesc"}
[Where we analyse the effect of a factor on shared diversity]{.hidden .quarto-markdown-envelope-contents render-id="quarto-ogcardddesc"}
:::




<!-- -->

::: {.quarto-embedded-source-code}
```````````````````{.markdown shortcodes="false"}
---
title: "Beta-diversity analysis"
subtitle: "Where we analyse the effect of a factor on shared diversity"
date: last-modified
author:
  - name: Adrien Taudière
    url: https://adrientaudiere.github.io/bioinfo.starter/analysis/02_alpha_diversity.qmd
    affiliation: IdEst
    affiliation-url: https://orcid.org/my-orcid?orcid=0000-0003-1088-1182
    citation: true
params:
  factor_of_interest: "Type"
# bibliography: bibliography.bib
# link-citations: true
---

See the documentation of the `MiscMetabar` package for example of [btea diversity analysis](https://adrientaudiere.github.io/MiscMetabar/articles/beta-div.html). 

quarto-executable-code-5450563D

```r
if(base::interactive()) {
  params <- rmarkdown::yaml_front_matter(here::here("analysis/03_beta_diversity.qmd"))$params
}
factor_of_interest <- params$factor_of_interest
```

```{r,  message=FALSE, warning=FALSE}
library(knitr)
library(targets)
library(MiscMetabar)
here::i_am("analysis/03_beta_diversity.qmd")
source(here::here("R/styles.R"))
```

quarto-executable-code-5450563D

```r
d_pq <- clean_pq(tar_read("d_vs", store=here::here("_targets/")))
```


quarto-executable-code-5450563D

```r
#| error: true
formattable_pq(
    subset_samples(d_pq, Type %in% c("Mix", "Mono")),
    factor_of_interest,
    min_nb_seq_taxa = 1000, 
    lev_col_taxa = "Family",
    taxonomic_levels=c("Order", "Family", "Genus"),
    log10trans = TRUE,

  )
```

quarto-executable-code-5450563D

```r
library("vegan")
plot_ordination(d_pq, vegan::decorana(vegdist(as(otu_table(d_pq), "matrix"),
    method = "robust.aitchison"
  )), color = factor_of_interest) +
  geom_point(size = 3) +
  stat_ellipse(inherit.aes = F, aes(x = DCA1, y = DCA2, linetype = .data[[factor_of_interest]], col = .data[[factor_of_interest]])) + theme_idest() + scale_color_manual(values=idest_pal$dark_color_idest[[1]][c(5,4,2)])
```


quarto-executable-code-5450563D

```r
adonis_pq(subset_samples(d_pq, Type %in% c("Mix", "Mono")), factor_of_interest, na_remove = TRUE, correction_for_sample_size = TRUE, by = "terms")
```


quarto-executable-code-5450563D

```r
d_pq |>
  subset_samples(Type %in% c("Mix", "Mono")) |>
biplot_pq(merge_sample_by = factor_of_interest, rarefy_after_merging = T)
```


quarto-executable-code-5450563D

```r
res_var <- var_par_rarperm_pq(
    subset_samples(d_pq, Type %in% c("Mix", "Mono")),
    list_component = list(
      "Tmt" = c("Tmt"),
      "Bloc" = c("Bloc"),
      "Type" = c("Type")
    ),
    nperm = 9,
    dbrda_computation = TRUE
  )

plot_var_part_pq(res_var)

{{< include _session_info.qmd >}} ``````````````````` :::